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<div class="title">MapStatistics </div> </div>
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<div class="textblock"><p>Extract extended statistics on the features of a map for quality control. </p>
<center></center><center><table class="doxtable">
<tr>
<td align="center" bgcolor="#EBEBEB">pot. predecessor tools </td><td valign="middle" rowspan="2"><img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> FileInfo <img class="formulaInl" alt="$ \longrightarrow $" src="form_91.png"/> </td><td align="center" bgcolor="#EBEBEB">pot. successor tools </td></tr>
<tr>
<td valign="middle" align="center" rowspan="1">FeatureFinder, FeatureMatcher </td><td valign="middle" align="center" rowspan="1">- </td></tr>
</table>
</center><p> This tool computes some basic statistics on the features of a map that are frequently used for quality control. In contrast to FileInfo</p>
<p>Information displayed includes:</p>
<ul>
<li>show information about the data range of a file (m/z, RT, intensity)</li>
<li>show a statistical summary for intensities, qualities, feature widths</li>
<li>break down the statistics for fractions of the map</li>
<li>total ion current included in the features as a function of RT</li>
</ul>
<p><b>The command line parameters of this tool are:</b> </p>
<pre class="fragment">
FileInfo -- Shows basic information about the file, such as data ranges and file type.
Version: 1.11.1 Nov 14 2013, 11:18:15, Revision: 11976
Usage:
FileInfo <options>
Options (mandatory options marked with '*'):
-in <file>* Input file (valid formats: 'mzData', 'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXM
L', 'consensusXML', 'idXML', 'pepXML', 'fid')
-in_type <type> Input file type -- default: determined from file extension or content (valid: 'mzData',
'mzXML', 'mzML', 'dta', 'dta2d', 'mgf', 'featureXML', 'consensusXML', 'idXML', 'pepXML',
'fid')
-out <file> Optional output file. If left out, the output is written to the command line. (valid
formats: 'txt')
-m Show meta information about the whole experiment
-p Shows data processing information
-s Computes a five-number statistics of intensities, qualities, and widths
-d Show detailed listing of all spectra and chromatograms (peak files only)
-c Check for corrupt data in the file (peak files only)
-v Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML
)
Common TOPP options:
-ini <file> Use the given TOPP INI file
-threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1')
-write_ini <file> Writes the default configuration file
--help Shows options
--helphelp Shows all options (including advanced)
</pre><p> <b>INI file documentation of this tool:</b> <div class="ini_global">
<div class="legend">
<b>Legend:</b><br>
<div class="item item_required">required parameter</div>
<div class="item item_advanced">advanced parameter</div>
</div>
<div class="node"><span class="node_name">+FileInfo</span><span class="node_description">Shows basic information about the file, such as data ranges and file type.</span></div>
<div class="item item_advanced"><span class="item_name" style="padding-left:16px;">version</span><span class="item_value">1.11.1</span>
<span class="item_description">Version of the tool that generated this parameters file.</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="node"><span class="node_name">++1</span><span class="node_description">Instance '1' section for 'FileInfo'</span></div>
<div class="item"><span class="item_name item_required" style="padding-left:24px;">in</span><span class="item_value"></span>
<span class="item_description">input file </span><span class="item_tags">input file</span><span class="item_restrictions">*.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">in_type</span><span class="item_value"></span>
<span class="item_description">input file type -- default: determined from file extension or content</span><span class="item_tags"></span><span class="item_restrictions">mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">out</span><span class="item_value"></span>
<span class="item_description">Optional output file. If left out, the output is written to the command line.</span><span class="item_tags">output file</span><span class="item_restrictions">*.txt</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">out_tsv</span><span class="item_value"></span>
<span class="item_description">Second optional output file. Tab separated flat text file.</span><span class="item_tags">output file</span><span class="item_restrictions">*.csv</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">m</span><span class="item_value">false</span>
<span class="item_description">Show meta information about the whole experiment</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">p</span><span class="item_value">false</span>
<span class="item_description">Shows data processing information</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">s</span><span class="item_value">false</span>
<span class="item_description">Computes a five-number statistics of intensities, qualities, and widths</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">d</span><span class="item_value">false</span>
<span class="item_description">Show detailed listing of all spectra and chromatograms (peak files only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">c</span><span class="item_value">false</span>
<span class="item_description">Check for corrupt data in the file (peak files only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item"><span class="item_name" style="padding-left:24px;">v</span><span class="item_value">false</span>
<span class="item_description">Validate the file only (for mzML, mzData, mzXML, featureXML, idXML, consensusXML, pepXML)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">log</span><span class="item_value"></span>
<span class="item_description">Name of log file (created only when specified)</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">debug</span><span class="item_value">0</span>
<span class="item_description">Sets the debug level</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item"><span class="item_name" style="padding-left:24px;">threads</span><span class="item_value">1</span>
<span class="item_description">Sets the number of threads allowed to be used by the TOPP tool</span><span class="item_tags"></span><span class="item_restrictions"> </span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">no_progress</span><span class="item_value">false</span>
<span class="item_description">Disables progress logging to command line</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div> <div class="item item_advanced"><span class="item_name" style="padding-left:24px;">test</span><span class="item_value">false</span>
<span class="item_description">Enables the test mode (needed for internal use only)</span><span class="item_tags"></span><span class="item_restrictions">true,false</span></div></div>
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<TD><font color="#c0c0c0">OpenMS / TOPP release 1.11.1</font></TD>
<TD align="right"><font color="#c0c0c0">Documentation generated on Thu Nov 14 2013 11:19:24 using doxygen 1.8.5</font></TD>
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